Clone Saga
by demented cookies
Summary: Someone is back. Someone that died many years ago. Someone that Artemis and Holly miss dearly. But when they learn more about him, they wish he had never left the underworld... R&R!
1. Chapter 1

Chapter one: Surprise

An elf walked silently down the quiet streets of Haven. His face was hidden in the shadows of the dark buildings. The roads were dimly lit by hanging streetlamps and the only fairies out, besides the elf, were goblins with smoking cigarettes in their wide mouths. He glowered menacingly at them. Their large eyes opened wide and cigarettes fell to the ground when their jaws dropped in astonishment. They scattered in all directions and into the dark alleyways.

Finally, the mysterious elf reached the building he was looking for…Police Plaza. He typed in a password on the password thingy but the doors remained closed. He tried again with the same result. He heard footsteps coming up from behind him and got ready to leap incase the newcomer brought trouble. He was right.

"May I help you, sir?" Major Trouble Kelp asked politely.

The elf spun around to face the Major. Trouble gasped when he saw the fairy's face.

"Doesn't it kinda look like I need help? How the blazes do I get in here?!" Commander Julius Root screamed.


	2. Meetings and Doubts

Chapter two: Meetings and Doubts

"C…Commander!" Trouble Kelp stuttered. Then he drew his neutrino and his face grew angry. "Whoever you are, lie face down on the ground with your hands behind your head."

"Trouble! What's wrong with you? You know me. It's Julius!"

"You must be pretty thick to think I'd fall for this gag. Commander Root's been dead for almost five years. But I'll give you an E for effort. You look awfully convincing."

"Major! Now you quit this stupid joke and let me in! I'm alive as ever, d'arvit!" His face was getting so red he looked like a strawberry.

"I'll also give you one chance to live. I'll count to three and if you're still here, then bang! You're gonna be dead as poor Julius."

"Don't call me that, Kelp! You know who I am!"

"Three…two…"

Julius knew he was fighting a pointless battle and so he decided to give up. "D'arvit." He murmured and left.

Walking down one of the lonelier streets he just happened to look up at the names of the buildings. _Jewel's Jewelry…Flowers and_ _Bulbs…Manure's Liquor…Short, Diggums and Day, Private Investigators…Laptops, Webcams and Other Prehistoric Inventi…_Wait! Commander Root stopped. Short, Diggums and Day? _Holly_ Short, _Mulch _Diggums and _Doodah_ Day?He jogged back a couple of paces and looked at the letters on the door to make sure he wasn't hallucinating. Surely enough, it was _Short, Diggums and Day, Private Investigators. _He tried the door and found it unlocked.

Julius entered and saw a tired looking Holly Short sitting behind a desk cluttered with papers and photos. Some photos were in frames. One of them was a portrait of the Commander himself. He smiled. His smile faded when he saw the words printed on the frame: "In Memory…"

His smile disappeared altogether when he saw the second picture on his desk. It was of Artemis Fowl, Butler, Mulch Diggums, Doodah Day, two fairies he didn't recognize, and Holly herself all standing close together like old friends. Even Artemis was smiling.

"Have a seat and I'll be with you in a minute." Holly said without looking up from the evidence photos she was holding in her left hand. With her right, she was scribbling down notes on a piece of paper.

Root didn't sit down. Instead, he stood, leaning on one foot with his arms crossed.

After what seemed like a century, Holly looked up from the photos. "Yes, may I…JULIUS!" She exclaimed. Her mouth fell open and her mismatched eyes grew large.

"Don't call me that!" The Commander yelled. He was really getting impatient.

"I…wha…you…er…" She stammered at loss for words. "You're supposed to be dead!"

"So I've been told." Root murmured.

"I…how did…?" Then her astonishment turned into a frown. "Who are you?"

"What do you mean?" He asked shocked. "You know exactly who I am!"

"Who are you?" She repeated, her eyes filling with tears for her late commander. "What do you want?"

"I…Holly…" This time it was Julius who couldn't find the right words.

"You're probably working for one of me and Artemis' enemies and want revenge or something."

"Captain! Must I go through with you what I went through with Kelp?"

Holly marched angrily to the door. "I know I can't get rid of you by myself so I'm callin' the cops." She picked up the phone by the door. Before she could dial, the Commander said, "Holly, you did save Artemis and Butler the way I told you to, didn't you?"

She paused, her finger barely touching the first number. Slowly, without looking at him, she put down the phone and stood there for a long time. Suddenly, she spun around and flew into Root's arms, wrapping him in a tight hug. "Yes," she whispered, "Yes I did."


	3. More Meetings than Doubts

Chapter three: More Doubts Than Meetings

It had been a year since Artemis got home from Hybras and so far his parents were taking it all very well. He and Butler had invented a generally believable story to tell about his absence. Juliet would take time off from wrestling to visit the Fowls which made her brother very happy. The twins, according to Mr. and Mrs. Fowl, were spitting images of Arty when he was younger and knew how to walk and talk (sort of) on their own by two years of age. But even while all this was going on, Artemis was looking unhappy. He would stay in his room for hours and when he wasn't there, he was wandering around the grounds looking thoughtful.

"Artemis, are you feeling alright?" Butler asked one day.

"I'm fine." Artemis replied.

"Are you sure? You look depressed."

"Really, I am fine."

"Okay…"

Artemis didn't want to tell him about his problem. Not yet. He didn't want to tell him that Holly had called him. Called him with news of Commander Root.

_Impossible, _he thought, _He couldn't come back from the dead. Clone? Clone? No. Clones are just like the original person except in a coma. I know there's something or someone behind this._

"What happened in the past few years while I was…gone?" Root and Holly were sitting in the waiting room of her office. "Leave not a single detail out."

"It's a _long_ story." Holly began. In a short three hours and seventeen minutes, she had told him the whole story. He smiled when she told him about how she and Artemis avenged his death and he grimed even wider when he heard about Artemis outsmarted Opal Koboi. His face fell when he heard about her quitting LEP and he listened attentively when she talked about finding the demons. He groaned and held his head in his hands when she told him about Minerva Paradizo. Holly told him about defeating Billy Kong and going to Hybras. She talked about the battle and how she was killed and Artemis saved her. Finally, she told the Commander how they found out that they had been gone for nearly three years and when Artemis got home he had twin siblings.

"Twins?!" Julius gasped. "His mother had twins?! Oh, no!"

"Don't worry. There still infants." Holly reassured him. "Besides, Artemis has changed over the years. In fact, he and I have become close friends."

Her warm smile was replaced with a thoughtful frown. "But I don't understand how you came back. I saw you die."

"I don't understand either." Julius said with a similar expression on his face. "I remember going through the terminal and ordering you to save the mudmen but what happened after that, I have no clue."

They sat in silence for a long time. Then Holly broke the silence. "I'm sorry." She smiled weakly. "did I say he changed over the _years_? I meant to say he changed over a matter of hours. You know, we only defeated Koboi with his determination to avenge your death."

Julius' exterior may have been serious and grim but on the inside he was beaming with happiness. Something that didn't happen often. Was it possible he had misjudged the mud boy?


	4. Intruder

Chapter four: Intruder

"Ha! Fools." Briar Cudgeon thought aloud. "They have no idea." He grinned an evil sinister grin. "With them thinking I'm dead, they haven't got a chance to beat me!"

After seeing his twin brother die at the hands of Opal Koboi, he fled but vowed revenge.

Cudgeon escaped aboveground to a small village for outlawed fairies on the outskirts of Asia and learned about an art suitable for revenge: cloning.

Presently, being and expert, he could get revenge on those he hated most. Namely, Holly Short, Artemis Fowl and Opal Koboi.

"Now where is my first clone?" Cudgeon said to himself. Looking through the iris cam his clone was wearing, he saw that it was speaking to Holly Short. Listening, he heard the clone say, "What happened in the past few years while I was…gone?"

Holly Short lay in bed puzzled. _How,_ she thought,_ how can Julius be back? Ghost? No. Couldn't be._ With that thought, she fell asleep.

Holly awoke to the sound of footsteps. Mistakenly letting her curiosity overcome her conscience, she got up pulling her robe around her.

She crept silent as a mouse down the stairs and into the living room. She ducked behind an armchair just in time to see a feminine figure come quietly into the room. The figure looked around as if searching for something not on the ground or under or on a table but head-height like a person.

The female intruder stopped and opened the door to her left, peering inside. Holly could tell from the way she looked around and stepped inside that she had found what she was looking for. That door happened to lead to the room Holly had offered to Root and the one he had accepted.


	5. Till Death Do Us Part

Chapter five: 'Till Death Do Us Part

The ex-captain was sitting in her room. She hadn't budged from that spot since she had spotted the intruder the night before in her apartment.

_Who was that? _She wondered, _what would she want with the commander. _

She heard voices downstairs. "No." said a voice which was obviously Root's.

"You must. You know the consequences." said a second voice. It sounded like…no. Couldn't be.

Holly stood and crept downstairs.

"I'm not doing it." The Commander sounded like he was resisting some kind of powerful force.

"You have to. _He_ says so. _He _wants you to." The mystery person emphasized the 'he' as if wanting to make it obvious that it was a substitute for the real name.

"You can't make me!"

"I can't, but _He _can."

"No! I will not obey him anymore!"

Holly looked closer. There was the commander and…no! Opal Koboi!

"No! I won't do as you or _He _says anymore! Never!"

Was the commander working for her?

"If not then I have no choice but…to kill you."

"No!" cried Holly as she leapt out into full view. She couldn't bear to witness her friend and former superior officer's death.

"Ah, Short. I've been hoping you'd come to see the 'Commander's' death."

"No!" Holly repeated. "He died once. He isn't going to die again."

"Oh, no." The pixie mocked. "He didn't die yet. Your dear 'Commander happens to be a clone."

"But he can't!"

"Oh, yes. _He_ knows how._ He _can make clones _live!_" She took a control device out from behind her. "Good bye, Julius." She said and pressed a button.

Immediately, Root keeled over and fell to the ground. Holly sprang to his side and rolled him onto his back. "Commander!" She cried. "Commander! Oh my god, Julius, speak to me!"

But she was too late. He was gone. Forever.


	6. Capture

Chapter six: Capture

Tears rolled down Holly's cheeks as she sat in her cell. _How could I have been so stupid? _She asked herself. _How could I have let Koboi kill him and capture me? _She dried her face but the tears kept coming. _I could have prevented this._

"Check mate." Artemis sighed as he made his fifth move.

"Darn." said Juliet. "Next time I'll get you."

"Right. But next time won't be soon because I'm going downstairs for some lunch."

"Well I'm gonna take the babies off your mother's hands." They both stood up and went their ways.

Butler made Artemis a quiche with caviar on the side. But the boy never ate it because, before he could take a bite, someone who looked remarkably like Opal Koboi snuck into the manor and knocked him out. With little effort, also ambushed Butler with chloroform from behind

"Oh, and you will find that the neutrino 3000 you borrowed is completely useless. I had _His_ clones demolish it." Opal said to Holly.

"When will this stop, Koboi?" Holly said through clenched teeth. "When will you quit this evil?"

"Isn't it obvious?" the villainous pixie laughed. Then she became serious. "When you're dead." She growled. She turned and left. Then everything went black…because she had turned off the light.


	7. Completely Harmless

Chapter seven: Completely Harmless

Artemis woke to the sound of Holly's voice. "Artemis," she said, "Artemis, wake up."

He sleepily opened his eyes. Seeing he wasn't in Fowl Manor, he looked around. The room was completely bare except for Holly, an unconscious Butler and himself. The walls and ceiling were white. The lights on the ceiling were rectangular and bright like in a hospital and the door into the other room was closed, supposedly locked.

"You're awake." Said a voice over the loudspeakers. It was female and pretty. But most importantly, it was recognizable. I was…

"Opal Koboi." Artemis growled, his voice soft but full of hatred and distrust. "Of course." Opal said calmly. "Who else would it be? Who else could devise a trap as perfect as the one you so have so gullibly fallen into?" She looked down at her pocket and reached inside without fear as though she thought Holly Short with her demolished and powerless neutrino 3000 and an out-of-breath Artemis and his unconscious bodyguard were completely harmless, which they were. She turned her gaze back at her victims and slowly, dramatically pulled out a device with a million little switches and buttons. In the center of the face of the controller was a large red switch.

She pressed a black button on the side of the tiny metal box and held it down.

"Prepare, my clones, for the moment we've been waiting for." She said speaking into the device. She then released the button and spoke to Artemis and Holly. She said, "I have waited a loooooong time for this.

"Get ready to die." She whispered just loud enough for them to hear. She pulled the red switch."


	8. Betrayal

Chapter eight: Betrayal 

Fortunately, Butler chose that moment to wake up. Butler leaped and dragged Holly and his employer to safety just as the flames of the explosion ricocheted off the walls. The noise was deafening, like a million explosions in one. Fire bounced around the room like a bouncy ball covered in water, leaving a little of itself wherever it went.

The three of them were able to avoid the flames by a hair. They barely got fried. Opal seeing that her murderous attempt had failed stormed into the now black with ash room to finish them off, carefully dodging the sparks. Holly stood there like an ex-captain should, head held high, fearless and ready for what might happen.

"You avoided me once too often." Opal fumed. "You won't this time."

Calmly, without taking her eyes off her enemy, Holly picked up a piece of her burnt, demolished neutrino. She drew back her arm and threw it as hard as she could at the pixie, which is pretty hard. The metal hit her square on her once pointed ear. Dead bull's-eye. She fell down unconscious. Artemis just stared wide-eyed. He looked at Holly, then at the fallen pixie, and right back at his friend.

Holly gazed down at her hand. I was red as a strawberry and smoking. She fell to her knees and held her hand in the other. "Ouch," she said to herself, "it hurts."

Artemis was focusing on his companion's hand rather than what was happening. "Artemis…" Butler said.

"Butler," Artemis replied annoyed. "Can you not tell the captain needs some assistance?"

"But, Artemis," Butler said again. "It's Koboi."

The boy sighed. "What is it?"

"She's," Butler said, "not breathing."

Artemis turned and saw he was right. "Well, at least she's not going to be trying to take over the world anytime soon."

"Maybe not her," another mysterious voice said. _This is getting really creepy._ Artemis thought to himself. "but she's not the only one."

"Who…?"

"Yes, I thought I'd have to tell you," the voice stated matter-of-factly, "since you believe me dead."

"Well, hurry up with it. We haven't got all day."

"You're right…because you're going to die before the sun goes down."

"As I said," Artemis said really getting annoyed, "hurry up. Quit the cliché."

"Alright," he said, "my name is…" You could almost hear dramatic music playing in the background. "Briar Cudgeon."

"Cudgeon?" Holly exclaimed, "But you're dead!"

"Told you so."

"I can't believe it!" Artemis said. "It's simply impossible!"

"Improbable, but not impossible," Cudgeon reminded him. "Now, enough small talk. It's show time! Clones, kill them, please."

Hundred of clones started filling the room from the single door. They lunged at Artemis and Butler. Not Holly, though. She was with them.


	9. The End?

Chapter nine: The End…?

Clones of Opal Koboi, Briar Cudgeon, Julius Root, and one Holly Short clawed at the two humans. Their eyes were foggy and distant as if they were being controlled by another. Which they were. Artemis huddled on the floor, hands over his head, and just lay there trembling while Butler held off the clones. He socked them in the face and kneed them in the stomach and threw them at the walls. He picked a Koboi up and threw her. She hit the wall with fatal force. She fell dead to the ground.

Butler kicked a Cudgeon in the jaw. The clone fell back for a moment then stood back up, his mouth was quite a few teeth short. Blood spilled from his jaw. He tackled again. Butler socked him in the stomach which knocked the wind out of the clone. Blood splattered on his shirt. Butler was able to hold them off for a long time but they were still too much for him. He fell to the ground unconscious. Artemis sat there shaking as the clones closed in on him…

"AAAAAAHHHHHH!" Artemis screamed as he sat up quick. His face was damp with sweat. He took a deep breath. _Just a nightmare,_ he tried telling himself, _just a nightmare._ The communicator on his bedside table rang. "Hello?" he said as he picked up the device.

"Artemis," Holly said with a bright expression on her face. He'd only seen her like that three times since the Commander's death.

"Yeah?"

"Great news! You'll never guess who showed up in my office today!"

"Who?"

She shoved another person in the small screen with her. Commander Root. "Unbelievable, isn't it?"

"Uh…yeah." Artemis croaked as his mind said _oh,no._


End file.
